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    228 results match your criteria Bioinformatics and Biology Insights [Journal]

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    Mathematical Model for Small Size Time Series Data of Bacterial Secondary Metabolic Pathways.
    Bioinform Biol Insights 2018 16;12:1177932218775076. Epub 2018 May 16.
    Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Waseda University, Tokyo, Japan.
    Measuring the concentrations of metabolites and estimating the reaction rates of each reaction step consisting of metabolic pathways are significant for an improvement in microorganisms used in maximizing the production of materials. Although the reaction pathway must be identified for such an improvement, doing so is not easy. Numerous reaction steps have been reported; however, the actual reaction steps activated vary or change according to the conditions. Read More

    Immune-Informatic Analysis and Design of Peptide Vaccine From Multi-epitopes Against .
    Bioinform Biol Insights 2018 14;12:1177932218755337. Epub 2018 May 14.
    Institute of Technology and Research, Universidade Tiradentes, Aracaju, Brazil.
    Caseous lymphadenitis (CLA) is a disease caused by bacteria that affects sheep and goats. The absence of a serologic diagnose is a factor that contributes for the disease dissemination, and due to the formation of granuloma, the treatment is very expensive. Therefore, prophylaxis is the approach with best cost-benefit relation; however, it still lacks an effective vaccine. Read More

    Lipophosphoglycan 3 From Binds Heparin With Micromolar Affinity.
    Bioinform Biol Insights 2018 13;12:1177932218763363. Epub 2018 Mar 13.
    Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, Brazil.
    is an intracellular protozoan parasite responsible for visceral leishmaniasis, a fatal disease in humans. Heparin-binding proteins (HBPs) are proteins that bind to carbohydrates present in glycoproteins or glycolipids. Evidence suggests that HBPs present on surface participate in the adhesion and invasion of parasites to tissues of both invertebrate and vertebrate hosts. Read More

    Review of Statistical Learning Methods in Integrated Omics Studies (An Integrated Information Science).
    Bioinform Biol Insights 2018 20;12:1177932218759292. Epub 2018 Feb 20.
    Department of Statistics, Faculty of Science, The University of Auckland, Auckland, New Zealand.
    Integrated omics is becoming a new channel for investigating the complex molecular system in modern biological science and sets a foundation for systematic learning for precision medicine. The statistical/machine learning methods that have emerged in the past decade for integrated omics are not only innovative but also multidisciplinary with integrated knowledge in biology, medicine, statistics, machine learning, and artificial intelligence. Here, we review the nontrivial classes of learning methods from the statistical aspects and streamline these learning methods within the statistical learning framework. Read More

    Analysis of Conserved, Computationally Predicted Epitope Regions for VP5 and VP7 Across three Orbiviruses.
    Bioinform Biol Insights 2018 31;12:1177932218755348. Epub 2018 Jan 31.
    Department of Life and Consumer Sciences, College of Agriculture and Environmental Sciences, University of South Africa, Roodepoort, South Africa.
    Orbiviruses are double-stranded RNA viruses that have profound economic and veterinary significance, 3 of the most important being African horse sickness virus (AHSV), bluetongue virus (BTV), and epizootic hemorrhagic disease virus (EHDV). Currently, vaccination and vector control are used as preventative measures; however, there are several problems with the current vaccines. Comparing viral amino acid sequences, we obtained an AHSV-BTV-EHDV consensus sequence for VP5 (viral protein 5) and for VP7 (viral protein 7) and generated homology models for these proteins. Read More

    In Silico Characterization and Functional Validation of Cell Wall Modification Genes Imparting Waterlogging Tolerance in Maize.
    Bioinform Biol Insights 2017 19;11:1177932217747277. Epub 2017 Dec 19.
    Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India.
    Cell wall modification (CWM) promotes the formation of aerenchyma in roots under waterlogging conditions as an adaptive mechanism. Lysigenous aerenchyma formation in roots improves oxygen transfer in plants, which highlights the importance of CWM as a focal point in waterlogging stress tolerance. We investigated the structural and functional compositions of CWM genes and their expression patterns under waterlogging conditions in maize. Read More

    R Script Approach to Infer Infection Mechanisms From Microarrays and Domain-Domain Protein Interactions.
    Bioinform Biol Insights 2017 17;11:1177932217747256. Epub 2017 Dec 17.
    Grupo de Estudio en Parasitología Molecular (GEPAMOL), Universidad del Quindío, Armenia, Colombia.
    Pathogen-host protein-protein interaction systems examine the interactions between the protein repertoires of 2 distinct organisms. Some of these pathogen proteins interact with the host protein system and may manipulate it for their own advantages. In this work, we designed an R script by concatenating 2 functions called rowDM and rowCVmed to infer pathogen-host interaction using previously reported microarray data, including host gene enrichment analysis and the crossing of interspecific domain-domain interactions. Read More

    Bioinformatic Analysis of Circadian Expression of Oncogenes and Tumor Suppressor Genes.
    Bioinform Biol Insights 2017 13;11:1177932217746991. Epub 2017 Dec 13.
    Department of Genetics, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran.
    Background: Circadian rhythms are physiological and behavioral cycles with a period of approximately 24 hours that control various functions including gene expression. Circadian disruption is associated with a variety of diseases, especially cancer. Although some of the oncogenes and tumor suppressor genes (TSGs) are known as clock-controlled genes (CCGs), the analysis and annotation of circadian expression of most human oncogenes and TSGs are still lacking. Read More

    Computational Model of the Effect of a Surface-Binding Site on the R64 α-Amylase to the Substrate Adsorption.
    Bioinform Biol Insights 2017 6;11:1177932217738764. Epub 2017 Nov 6.
    Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Sumedang, Indonesia.
    α-Amylase is one of the important enzymes in the starch-processing industry. However, starch processing requires high temperature, thus resulting in high cost. The high adsorptivity of α-amylase to the substrate allows this enzyme to digest the starch at a lower temperature. Read More

    Finding the Sources of Missing Heritability within Rare Variants Through Simulation.
    Bioinform Biol Insights 2017 4;11:1177932217735096. Epub 2017 Oct 4.
    BDX Research & Consulting LLC, Fairfax, VA, USA.
    Thousands of genome-wide association studies (GWAS) have been conducted to identify the genetic variants associated with complex disorders. However, only a small proportion of phenotypic variances can be explained by the reported variants. Moreover, many GWAS failed to identify genetic variants associated with disorders displaying hereditary features. Read More

    A Metagenomic Analysis of Bacterial Microbiota in the Digestive Tract of Triatomines.
    Bioinform Biol Insights 2017 27;11:1177932217733422. Epub 2017 Sep 27.
    Laboratório de Bioquímica e Fisiologia de Insetos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (IOC/FIOCRUZ), Rio de Janeiro, Brazil.
    The digestive tract of triatomines (DTT) is an ecological niche favored by microbiota whose enzymatic profile is adapted to the specific substrate availability in this medium. This report describes the molecular enzymatic properties that promote bacterial prominence in the DTT. The microbiota composition was assessed previously based on 16S ribosomal DNA, and whole sequenced genomes of bacteria from the same genera were used to calculate the GC level of rare and prominent bacterial species in the DTT. Read More

    Bioinformatics Study of m.9053G>A Mutation at the Gene in Relation to Type 2 Diabetes Mellitus and Cataract Diseases.
    Bioinform Biol Insights 2017 12;11:1177932217728515. Epub 2017 Sep 12.
    Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Bandung, Indonesia.
    The mitochondrial disease often associated with various illnesses in relation to the activity of cells metabolites and the synthesis of adenosine triphosphate (ATP), including alteration in the mitochondrial DNA. The mutation of m.9053G>A at the gene was found in patients with type 2 diabetes mellitus (DM type 2) and cataract. Read More

    Reverse Nearest Neighbor Search on a Protein-Protein Interaction Network to Infer Protein-Disease Associations.
    Bioinform Biol Insights 2017 13;11:1177932217720405. Epub 2017 Jul 13.
    Advanced Virtual and Intelligent Computing (AVIC) Center, Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok, Thailand.
    The associations between proteins and diseases are crucial information for investigating pathological mechanisms. However, the number of known and reliable protein-disease associations is quite small. In this study, an analysis framework to infer associations between proteins and diseases was developed based on a large data set of a human protein-protein interaction network integrating an effective network search, namely, the reverse -nearest neighbor (RNN) search. Read More

    CellTrans: An R Package to Quantify Stochastic Cell State Transitions.
    Bioinform Biol Insights 2017 16;11:1177932217712241. Epub 2017 Jun 16.
    Fakultät Informatik/Mathematik, Hochschule für Technik und Wirtschaft Dresden, Dresden, Germany.
    Many normal and cancerous cell lines exhibit a stable composition of cells in distinct states which can, e.g., be defined on the basis of cell surface markers. Read More

    A Computational Methodology to Overcome the Challenges Associated With the Search for Specific Enzyme Targets to Develop Drugs Against .
    Bioinform Biol Insights 2017 12;11:1177932217712471. Epub 2017 Jun 12.
    Laboratório de Modelagem de Sistemas Biológicos, Instituto Nacional de Ciência e Tecnologia de Inovação em Doenças de Populações Negligenciadas (INCT-IDPN), Centro de Desenvolvimento Tecnológico em Saúde (CDTS), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil.
    We present an approach for detecting enzymes that are specific of compared with and provide targets that may assist research in drug development. This approach is based on traditional techniques of sequence homology comparison by similarity search and Markov modeling; it integrates the characterization of enzymatic functionality, secondary and tertiary protein structures, protein domain architecture, and metabolic environment. From 67 enzymes represented by 42 enzymatic activities classified by AnEnPi (Analogous Enzymes Pipeline) as specific for compared with , only 40 (23 Enzyme Commission [EC] numbers) could actually be considered as strictly specific of and 27 enzymes (19 EC numbers) were disregarded for having ambiguous homologies or analogies with . Read More

    Prepartal Energy Intake Alters Blood Polymorphonuclear Leukocyte Transcriptome During the Peripartal Period in Holstein Cows.
    Bioinform Biol Insights 2017 28;11:1177932217704667. Epub 2017 Apr 28.
    Division of Nutritional Sciences, Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
    In the dairy industry, cow health and farmer profits depend on the balance between diet (ie, nutrient composition, daily intake) and metabolism. This is especially true during the transition period, where dramatic physiological changes foster vulnerability to immunosuppression, negative energy balance, and clinical and subclinical disorders. Using an Agilent microarray platform, this study examined changes in the transcriptome of bovine polymorphonuclear leukocytes (PMNLs) due to prepartal dietary intake. Read More

    In Silico Approach for Characterization and Comparison of Repeats in the Genomes of Oil and Date Palms.
    Bioinform Biol Insights 2017 18;11:1177932217702388. Epub 2017 Apr 18.
    Graduate Program in Plant Biotechnology, Federal University of Lavras (UFLA), Lavras, Brazil.
    Transposable elements (TEs) are mobile genetic elements present in almost all eukaryotic genomes. Due to their typical patterns of repetition, discovery, and characterization, they demand analysis by various bioinformatics software. Probably, as a result of the need for a complex analysis, many genomes publicly available do not have these elements annotated yet. Read More

    An Insight Into Structure, Function, and Expression Analysis of 3-Hydroxy-3-Methylglutaryl-CoA Reductase of .
    Bioinform Biol Insights 2017 30;11:1177932217701735. Epub 2017 Mar 30.
    Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, India.
    Citronella () is one of the richest sources of high-value isoprenoid aromatic compounds used as flavour, fragrance, and therapeutic elements. These isoprenoid compounds are synthesized by 2 independent pathways: mevalonate pathway and 2-C-methyl-d-erythritol-4-phosphate pathway. Evidence suggests that 3-hydroxy-3-methylglutaryl-CoA reductase (HMGR) is a rate-controlling enzyme for the synthesis of variety of isoprenoids. Read More

    PISMA: A Visual Representation of Motif Distribution in DNA Sequences.
    Bioinform Biol Insights 2017 30;11:1177932217700907. Epub 2017 Mar 30.
    Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), México City, México.
    Background: Because the graphical presentation and analysis of motif distribution can provide insights for experimental hypothesis, PISMA aims at identifying motifs on DNA sequences, counting and showing them graphically. The motif length ranges from 2 to 10 bases, and the DNA sequences range up to 10 kb. The motif distribution is shown as a bar-code-like, as a gene-map-like, and as a transcript scheme. Read More

    Plasma MicroRNA Levels Following Resection of Metastatic Melanoma.
    Bioinform Biol Insights 2017 23;11:1177932217694837. Epub 2017 Feb 23.
    Department of Surgery, The Ohio State University, Columbus, OH, USA.
    Melanoma remains the leading cause of skin cancer-related deaths. Surgical resection and adjuvant therapies can result in disease-free intervals for stage III and stage IV disease; however, recurrence is common. Understanding microRNA (miR) dynamics following surgical resection of melanomas is critical to accurately interpret miR changes suggestive of melanoma recurrence. Read More

    Transcriptologs: A Transcriptome-Based Approach to Predict Orthology Relationships.
    Bioinform Biol Insights 2017 23;11:1177932217690136. Epub 2017 Feb 23.
    Department of Agriculture, University of Naples "Federico II," Portici, Italy.
    The detection of orthologs is a key approach in genomics, useful to understand gene evolution and phylogenetic relationships and essential for gene function prediction. However, a reliable annotation of the encoded protein regions is still a limiting aspect in genomics, mainly due to the lack of confirmatory experimental evidence at proteome level. Nevertheless, the current ortholog collections are generally based on protein sequence comparisons, in addition to the availability of large transcriptome sequence collections. Read More

    Current Developments in Machine Learning Techniques in Biological Data Mining.
    Bioinform Biol Insights 2017 22;11:1177932216687545. Epub 2017 Mar 22.
    Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, USA.
    This supplement is intended to focus on the use of machine learning techniques to generate meaningful information on biological data. This supplement under aims to provide scientists and researchers working in this rapid and evolving field with online, open-access articles authored by leading international experts in this field. Advances in the field of biology have generated massive opportunities to allow the implementation of modern computational and statistical techniques. Read More

    Molecular Modeling and Phylogeny of the Krüppel-like Factor 4 (cKLF4) Protein from the Arabian Camel, .
    Bioinform Biol Insights 2016 21;10:291-300. Epub 2016 Dec 21.
    National Center for Genomic Technology, King Abdulaziz City for Science and Technology, Riyadh, Kingdom of Saudi Arabia.
    Krüppel-like factor 4 (KLF4) is a pluripotency transcription factor that helps in generating induced pluripotent stem cells (iPSCs). We sequenced for the first time the full coding sequence of KLF4 (cKLF4), which is also known as the Arabian camel. Bioinformatics analysis revealed the molecular weight and the isoelectric point of cKLF4 protein to be 53. Read More

    Integrating Epigenomics into the Understanding of Biomedical Insight.
    Bioinform Biol Insights 2016 4;10:267-289. Epub 2016 Dec 4.
    Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.; Present address: Department of Medical Genetics, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
    Epigenetics is one of the most rapidly expanding fields in biomedical research, and the popularity of the high-throughput next-generation sequencing (NGS) highlights the accelerating speed of epigenomics discovery over the past decade. Epigenetics studies the heritable phenotypes resulting from chromatin changes but without alteration on DNA sequence. Epigenetic factors and their interactive network regulate almost all of the fundamental biological procedures, and incorrect epigenetic information may lead to complex diseases. Read More

    Analysis of Parallel Algorithms on SMP Node and Cluster of Workstations Using Parallel Programming Models with New Tile-based Method for Large Biological Datasets.
    Bioinform Biol Insights 2016 30;10:255-265. Epub 2016 Nov 30.
    Department of Computer Science and Engineering, Visvesvaraya National Institute of Technology, Nagpur, India.
    Sequence alignment is an important tool for describing the relationships between DNA sequences. Many sequence alignment algorithms exist, differing in efficiency, in their models of the sequences, and in the relationship between sequences. The focus of this study is to obtain an optimal alignment between two sequences of biological data, particularly DNA sequences. Read More

    Clustering Algorithms: Their Application to Gene Expression Data.
    Bioinform Biol Insights 2016 30;10:237-253. Epub 2016 Nov 30.
    Department of Computer and Information Sciences, Covenant University, Ota, Ogun State, Nigeria.; Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State, Nigeria.
    Gene expression data hide vital information required to understand the biological process that takes place in a particular organism in relation to its environment. Deciphering the hidden patterns in gene expression data proffers a prodigious preference to strengthen the understanding of functional genomics. The complexity of biological networks and the volume of genes present increase the challenges of comprehending and interpretation of the resulting mass of data, which consists of millions of measurements; these data also inhibit vagueness, imprecision, and noise. Read More

    An Empirical Prior Improves Accuracy for Bayesian Estimation of Transcription Factor Binding Site Frequencies within Gene Promoters.
    Bioinform Biol Insights 2015 25;9(Suppl 4):59-69. Epub 2016 Oct 25.
    Department of Biomedical Sciences, Oregon State University, Corvallis, OR, USA.; School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR, USA.
    A Bayesian method for sampling from the distribution of matches to a precompiled transcription factor binding site (TFBS) sequence pattern (conditioned on an observed nucleotide sequence and the sequence pattern) is described. The method takes a position frequency matrix as input for a set of representative binding sites for a transcription factor and two sets of noncoding, 5' regulatory sequences for gene sets that are to be compared. An empirical prior on the frequency A (per base pair of gene-vicinal, noncoding DNA) of TFBSs is developed using data from the ENCODE project and incorporated into the method. Read More

    Structural Prediction and Physicochemical Characterization for Mouse Caltrin I and Bovine Caltrin Proteins.
    Bioinform Biol Insights 2016 30;10:225-236. Epub 2016 Oct 30.
    Instituto de Investigaciones Biológicas y Tecnológicas (IIByT) CONICET-Universidad Nacional de Córdoba, and Instituto de Ciencia y Tecnología de los Alimentos (ICTA), Cátedra de Química Biológica, Departamento de Química Industrial y Aplicada, Facultad de Ciencias Exactas, Físicas y Naturales, Córdoba, Argentina.
    It is known that caltrin (calcium transport inhibitor) protein binds to sperm cells during ejaculation and inhibits extracellular Ca uptake. Although the sequence and some biological features of mouse caltrin I and bovine caltrin are known, their physicochemical properties and tertiary structure are mainly unknown. We predicted the 3D structures of mouse caltrin I and bovine caltrin by molecular homology modeling and threading. Read More

    Iterative Fragmentation Improves the Detection of ChIP-seq Peaks for Inactive Histone Marks.
    Bioinform Biol Insights 2016 25;10:209-224. Epub 2016 Oct 25.
    Researcher, R&D Epigenetics Department of Diagenode SA, Liège, Belgium.
    As chromatin immunoprecipitation (ChIP) sequencing is becoming the dominant technique for studying chromatin modifications, new protocols surface to improve the method. Bioinformatics is also essential to analyze and understand the results, and precise analysis helps us to identify the effects of protocol optimizations. We applied iterative sonication - sending the fragmented DNA after ChIP through additional round(s) of shearing - to a number of samples, testing the effects on different histone marks, aiming to uncover potential benefits of inactive histone marks specifically. Read More

    Survey of Genes Involved in Biosynthesis, Transport, and Signaling of Phytohormones with Focus on .
    Bioinform Biol Insights 2016 26;10:185-207. Epub 2016 Sep 26.
    Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany.; Cluster of Excellence Macromolecular Complexes, Institute for Molecular Cell Biology of Plants, Frankfurt am Main, Germany.
    Phytohormones control the development and growth of plants, as well as their response to biotic and abiotic stress. The seven most well-studied phytohormone classes defined today are as follows: auxins, ethylene, cytokinin, abscisic acid, jasmonic acid, gibberellins, and brassinosteroids. The basic principle of hormone regulation is conserved in all plants, but recent results suggest adaptations of synthesis, transport, or signaling pathways to the architecture and growth environment of different plant species. Read More

    Evolution of Synonymous Codon Usage in the Mitogenomes of Certain Species of Bilaterian Lineage with Special Reference to Chaetognatha.
    Bioinform Biol Insights 2016 22;10:167-84. Epub 2016 Sep 22.
    Aushmath Biosciences, Administrative office, Devaraj Corner, Vadavalli Post, Coimbatore, Tamil Nadu, India.
    Chaetognatha is a minor phylum, comprising transparent marine invertebrates varying in size from 0.5 to 12 cm. The exact phylogenetic position of Chaetognatha in Metazoa has not been deciphered as some embryological characteristics place chaetognaths among deuterostomes and some morphological characteristics place these among protostomes. Read More

    Interaction Analysis of T7 RNA Polymerase with Heparin and Its Low Molecular Weight Derivatives - An In Silico Approach.
    Bioinform Biol Insights 2016 29;10:155-66. Epub 2016 Aug 29.
    Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India.
    The single subunit T7 RNA polymerase (T7RNAP) is a model enzyme for studying the transcription process and for various biochemical and biophysical studies. Heparin is a commonly used inhibitor against T7RNAP and other RNA polymerases. However, exact interaction between heparin and T7RNAP is still not completely understood. Read More

    In Silico Structure Prediction of Human Fatty Acid Synthase-Dehydratase: A Plausible Model for Understanding Active Site Interactions.
    Bioinform Biol Insights 2016 14;10:143-54. Epub 2016 Aug 14.
    Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Rajasthan, India.
    Fatty acid synthase (FASN, UniProt ID: P49327) is a multienzyme dimer complex that plays a critical role in lipogenesis. Consequently, this lipogenic enzyme has gained tremendous biomedical importance. The role of FASN and its inhibition is being extensively researched in several clinical conditions, such as cancers, obesity, and diabetes. Read More

    OSG-GEM: Gene Expression Matrix Construction Using the Open Science Grid.
    Bioinform Biol Insights 2016 2;10:133-41. Epub 2016 Aug 2.
    Department of Genetics and Biochemistry, Clemson University, SC, USA.
    High-throughput DNA sequencing technology has revolutionized the study of gene expression while introducing significant computational challenges for biologists. These computational challenges include access to sufficient computer hardware and functional data processing workflows. Both these challenges are addressed with our scalable, open-source Pegasus workflow for processing high-throughput DNA sequence datasets into a gene expression matrix (GEM) using computational resources available to U. Read More

    Computational Identification of Novel Genes: Current and Future Perspectives.
    Bioinform Biol Insights 2016 1;10:121-31. Epub 2016 Aug 1.
    Institute for Evolution and Biodiversity, Westfalian Wilhelms University Muenster, Huefferstrasse 1, Muenster, Germany.
    While it has long been thought that all genomic novelties are derived from the existing material, many genes lacking homology to known genes were found in recent genome projects. Some of these novel genes were proposed to have evolved de novo, ie, out of noncoding sequences, whereas some have been shown to follow a duplication and divergence process. Their discovery called for an extension of the historical hypotheses about gene origination. Read More

    Phylogenetic and Structural Analysis of the Pluripotency Factor Sex-Determining Region Y box2 Gene of Camelus dromedarius (cSox2).
    Bioinform Biol Insights 2016 26;10:111-20. Epub 2016 Jul 26.
    National Center for Stem Cell Technology, King Abdulaziz City for Science and Technology, Riyadh, KSA.; SAAD Research and Development Center, Clinical Research Laboratory and Radiation Oncology, SAAD Specialist Hospital, Al Khobar, KSA.
    Although the sequencing information of Sox2 cDNA for many mammalian is available, the Sox2 cDNA of Camelus dromedaries has not yet been characterized. The objective of this study was to sequence and characterize Sox2 cDNA from the brain of C. dromedarius (also known as Arabian camel). Read More

    PIMADb: A Database of Protein-Protein Interactions in Huge Macromolecular Assemblies.
    Bioinform Biol Insights 2016 19;10:105-9. Epub 2016 Jul 19.
    National Centre for Biological Sciences (TIFR), GKVK Campus, Bangalore, India.
    Protein-protein interactions play a very important role in the process of cellular functionality. Intricate details about the interactions between the proteins in a macromolecular assembly are important to understand the function and significance of protein complexes. We are reporting about a database of protein-protein interactions in huge macromolecular assemblies (PIMADb) that records the intrinsic details of 189,532 interchain interactions in 40,049 complexes from the Protein Data Bank. Read More

    Molecular Shape Analysis-Guided Virtual Screening Platform for Adenosine Kinase Inhibitors.
    Bioinform Biol Insights 2016 18;10:97-103. Epub 2016 Jul 18.
    Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India.
    We propose a new application of molecular shape descriptors in hierarchical selection during virtual screening (VS). Here, a structure-based pharmacophore and docking-guided VS protocol have been evolved to identify inhibitors against adenosine kinase (AK). The knowledge gained on the shape requirements has been extrapolated in classifying active and inactive molecules against this target. Read More

    S2M: A Stochastic Simulation Model of Poliovirus Genetic State Transition.
    Bioinform Biol Insights 2016 27;10:81-95. Epub 2016 Jun 27.
    Computation Applications and Research Department, Lawrence Livermore National Laboratory, Livermore, CA, USA.
    Modeling the molecular mechanisms that govern genetic variation can be useful in understanding the dynamics that drive genetic state transition in quasispecies viruses. For example, there is considerable interest in understanding how the relatively benign vaccine strains of poliovirus eventually revert to forms that confer neurovirulence and cause disease (ie, vaccine-derived poliovirus). This report describes a stochastic simulation model, S2M, which can be used to generate hypothetical outcomes based on known mechanisms of genetic diversity. Read More

    PDBparam: Online Resource for Computing Structural Parameters of Proteins.
    Bioinform Biol Insights 2016 14;10:73-80. Epub 2016 Jun 14.
    Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India.
    Understanding the structure-function relationship in proteins is a longstanding goal in molecular and computational biology. The development of structure-based parameters has helped to relate the structure with the function of a protein. Although several structural features have been reported in the literature, no single server can calculate a wide-ranging set of structure-based features from protein three-dimensional structures. Read More

    Genome Data Exploration Using Correspondence Analysis.
    Bioinform Biol Insights 2016 7;10:59-72. Epub 2016 Jun 7.
    Institut Pasteur, Unit of Structural Microbiology, CNRS URA 3528 and University Paris Diderot, Sorbonne Paris Cité, Paris, France.
    Recent developments of sequencing technologies that allow the production of massive amounts of genomic and genotyping data have highlighted the need for synthetic data representation and pattern recognition methods that can mine and help discovering biologically meaningful knowledge included in such large data sets. Correspondence analysis (CA) is an exploratory descriptive method designed to analyze two-way data tables, including some measure of association between rows and columns. It constructs linear combinations of variables, known as factors. Read More

    Modeling of the Glycolysis Pathway in Plasmodium falciparum using Petri Nets.
    Bioinform Biol Insights 2016 12;10:49-57. Epub 2016 May 12.
    Department of Computer and Information Sciences, Covenant University, Ota, Ogun State, Nigeria.
    Malaria is one of the deadly diseases, which affects a large number of the world's population. The Plasmodium falciparum parasite during erythrocyte stages produces its energy mainly through anaerobic glycolysis, with pyruvate being converted into lactate. The glycolysis metabolism in P. Read More

    Practical Approaches for Mining Frequent Patterns in Molecular Datasets.
    Bioinform Biol Insights 2016 2;10:37-47. Epub 2016 May 2.
    Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium.; Biomedical Informatics Research Center Antwerpen (Biomina), University of Antwerp/Antwerp University Hospital, Antwerp, Belgium.
    Pattern detection is an inherent task in the analysis and interpretation of complex and continuously accumulating biological data. Numerous itemset mining algorithms have been developed in the last decade to efficiently detect specific pattern classes in data. Although many of these have proven their value for addressing bioinformatics problems, several factors still slow down promising algorithms from gaining popularity in the life science community. Read More

    Vaccine Design for H5N1 Based on B- and T-cell Epitope Predictions.
    Bioinform Biol Insights 2016 28;10:27-35. Epub 2016 Apr 28.
    Mathematics Computation Group, Department of Mathematics, Faculty of Mathematics and Natural Science, University of Indonesia, Depok, Indonesia.
    From 2003 to 2013, Indonesia had the highest number of avian influenza A cases in humans, with 192 cases and 160 fatalities. Avian influenza is caused by influenza virus type A, such as subtype H5N1. This virus has two glycoproteins: hemagglutinin and neuraminidase, which will become the primary target to be neutralized by vaccine. Read More

    Use of Metatranscriptomics in Microbiome Research.
    Bioinform Biol Insights 2016 20;10:19-25. Epub 2016 Apr 20.
    Department of Immunology, Weizmann Institute of Science, Rehovot, Israel.
    The human intestinal microbiome is a microbial ecosystem that expresses as many as 100 times more genes than the human host, thereby constituting an important component of the human holobiome, which contributes to multiple health and disease processes. As most commensal species are difficult or impossible to culture, genomic characterization of microbiome composition and function, under various environmental conditions, comprises a central tool in understanding its roles in health and disease. The first decade of microbiome research was mainly characterized by usage of DNA sequencing-based 16S rDNA and shotgun metagenome sequencing, allowing for the elucidation of microbial composition and genome structure. Read More

    Modeling Intercellular Communication as a Survival Strategy of Cancer Cells: An In Silico Approach on a Flexible Bioinformatics Framework.
    Bioinform Biol Insights 2016 13;10:5-18. Epub 2016 Mar 13.
    Facultad de Medicina, Benemérita Universidad Autónoma de Puebla, Puebla, México.
    Intercellular communication is very important for cell development and allows a group of cells to survive as a population. Cancer cells have a similar behavior, presenting the same mechanisms and characteristics of tissue formation. In this article, we model and simulate the formation of different communication channels that allow an interaction between two cells. Read More

    Transcriptome Analysis in Domesticated Species: Challenges and Strategies.
    Bioinform Biol Insights 2015 16;9(Suppl 4):21-31. Epub 2016 Feb 16.
    Department of Animal Sciences, College of ACES, University of Illinois at Urbana-Champaign, Urbana, USA.
    Domesticated species occupy a special place in the human world due to their economic and cultural value. In the era of genomic research, domesticated species provide unique advantages for investigation of diseases and complex phenotypes. RNA sequencing, or RNA-seq, has recently emerged as a new approach for studying transcriptional activity of the whole genome, changing the focus from individual genes to gene networks. Read More

    Visualization of Genome Diversity in German Shepherd Dogs.
    Bioinform Biol Insights 2015 10;9(Suppl 2):37-42. Epub 2016 Feb 10.
    Faculty of Veterinary Science, The University of Sydney, NSW, Australia.
    A loss of genetic diversity may lead to increased disease risks in subpopulations of dogs. The canine breed structure has contributed to relatively small effective population size in many breeds and can limit the options for selective breeding strategies to maintain diversity. With the completion of the canine genome sequencing project, and the subsequent reduction in the cost of genotyping on a genomic scale, evaluating diversity in dogs has become much more accurate and accessible. Read More

    Nematode Sodium Calcium Exchangers: A Surprising Lack of Transport.
    Bioinform Biol Insights 2016 1;10:1-4. Epub 2016 Feb 1.
    Department of Biological Sciences, The George Washington University, Washington, DC, USA.; Institute for Neuroscience, The George Washington University, Washington, DC, USA.
    Na(+)/Ca(2+) exchangers are low-affinity, high-capacity transporters that rapidly transport calcium against a gradient of Na(+) ions. Na(+)/Ca(2+) exchangers are divided into three groups based upon substrate specificity: Na(+)/Ca(2+) exchangers (NCX), Na(+)/Ca(2+)/K(+) exchangers (NCKX), and Ca(2+)/cation exchangers (NCLX). In mammals, there are three NCX genes, five NCKX genes, and a single NCLX gene. Read More

    Effects of Pseudorabies Virus Infection on the Tracheobronchial Lymph Node Transcriptome.
    Bioinform Biol Insights 2015 24;9(Suppl 2):25-36. Epub 2016 Jan 24.
    Virus and Prion Research Unit, National Animal Disease Center, USDA, Agricultural Research Service, Ames, IA, USA.
    This study represents the first swine transcriptome hive plots created from gene set enrichment analysis (GSEA) data and provides a novel insight into the global transcriptome changes occurring in tracheobronchial lymph nodes (TBLN) and spanning the swine genome. RNA isolated from draining TBLN from 5-week-old pigs, either clinically infected with a feral isolate of Pseudorabies virus or uninfected, was interrogated using Illumina Digital Gene Expression Tag Profiling. More than 100 million tag sequences were observed, representing 4,064,189 unique 21-base sequences collected from TBLN at time points 1, 3, 6, and 14 days post-inoculation (dpi). Read More

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